My group has identified thousands of genomic insertion/deletion ("indel") dimorphisms that distinguish different inbred mouse strains. We found that a majority of larger dimorphic indels is due to recent retrotransposition, particularly by L1 (LINE) retrotransposons. All candidate dimorphisms queried have been validated by a PCR assay. The dimorphic transposons have all the typical features of bona fide recent integration events including target site duplications, canonical target specificity, long poly(A) tails, preferential localization within gene introns antisense to gene orientation, and length distribution. We also identified numerous novel transcript structures, attributable directly to some of these recently integrated transposons. We also developed a new molecular technique to identify newly mobilized endogenous transposons, and showed that human L1 elements actively move in cultured cancer cell lines within a few weeks. These results show that transposons can alter the normal mammalian genome, and gene expression profiles, dramatically and in real time. A disproportionate number of dimorphic endogenous transposons in mouse strains are located in or near genes expressed in brain. Numerous novel transcript structures, attributable directly to recent transposon integrants, are specifically expressed in brain and/or testis. Most endogenous transposons are expressed in only certain tissues, typically early in development, such as brain and testis. Additionally, my group has developed a cultured cell-based experimental system to study epigenetic control of mammalian retrotransposons. Using a marked L1 retrotransposon, we have studied the mechanism of variegation and silencing of L1 reporters that are newly inserted via a retrotransposition-dependent mechanism in tissue culture cells. We found that DNA methylation does not play a major role in silencing of these new integrants, but rather that dynamically regulated histone acetylation and deacetylation are correlated with variable reporter expression. We have modified a procedure to introduce reporters together with fragments of other elements such as insulators, retrotransposons, etc. into defined genetic loci, i.e. recombination-mediated cassette exchange. We have successfully sequenced and analyzed several full Serial Analysis of Gene Expression (SAGE) long-tag libraries to characterize global transcript levels, including those corresponding to repetitive and transposable elements, in somatic cells with altered epigenetic controls. The libraries completed to date include numerous transcripts that are differentially expressed at very high ratios. Numerous differentially expressed transcripts have been identified and validated by independent techniques including Northern blotting and quantitative polymerase chain reaction (qPCR) experiments, including members of several gene families or pathways such as cancer testis genes, interferon-inducibile genes, major histocompatibility complex (MHC) genes, and the metallothionein gene cluster. We are now further characterizing how altered expression may be related to changes in epigenetic control.